The New Zealand-born fly-half tore the anterior cruciate ligament in his right knee in the 22nd minute of Australia's 21-18 victory over Wales in Friday's World Cup third-place play- off.
The Reds star visited his surgeon in Brisbane on Sunday.
As a result of the consultation, the 23-year-old will undergo an MRI scan in the coming days before having surgery to reconstruct the ACL, while also repairing his lateral ligament.
The best-case scenario of six months would see the playmaker return in early May, meaning he will miss at least the first 10 rounds of the Reds' Super 15 title defence.
He will also miss the Wallabies' next two fixtures against the Barbarians at Twickenham on November 26 and Wales at Millennium Stadium on December 3.
Berrick Barnes claims he is ready to replace Cooper on Australia's end-of-season tour, having exceeded his own expectations during the World Cup.
Barnes, omitted from the starting side in the quarter-final and semi-final, made the most of his call-up to XV against Wales with a man-of-the-match performance.
The 25-year-old scored the opening try and was impressive in defence and would appear to be in pole position for the fly-half role against the Barbarians and Wales.
"If that offer presented I'd be happy to step up and have a crack," Barnes said.
"They're tough Tests for sure and we see Wales a hell of a lot in the next few months and a lot of those boys will probably be involved in the Baa Baas - Jamie Roberts and these sorts of blokes tend to go pretty well for them.
"Playing Wales at home with obviously Sam Warburton back and Adam Jones, we'll see a different side and we're going to have some cattle probably staying at home as well."
Barnes endured a well-publicised battle with the footballers' migraine condition in 2011 and was forced to take an indefinite break from the game in June.
He admits he had major doubts over his ability to make his way back in time for his second World Cup campaign.
"It's massive, I didn't think I'd be here and I told (coach) Robbie (Deans) when I took time off that the World Cup was the last thing on my mind," he said.
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